PRO Consortium Workshop 2017
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Date: October 11-12, 2017
Venue: Atlantic Oceanside Hotel, Bar Harbor, MN
Goals
The goals of this meeting are:
- 1. To review the current state of the Protein Ontology and its relation to other protein-related information resources, especially UniProt and GO and to document these relations with a view to publication.
- 2. To evaluate current competing approaches to gene annotation in PRO and in other OBO Foundry ontologies and to document the implications of this evaluation with a view to publication.
- 3. To assess progress in the use of advanced computational techniques, including Natural Language Processing, in the development of the PRO.
- 4. To examine the actual and potential contribution of PRO to the understanding of disease across organisms.
- 5. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis.
Schedule: Tuesday, October, 10, 2017
19:00 Informal reception for early arrivals in conference hotel
Schedule: Wednesday, October, 11, 2017
Introductory Session: The Landscape of the Protein Ontology
- 8:45 Cathy Wu: Protein Ontology: Its current state and future development
- 9:30 Susan Gregurick: NIH 2018 Priorities in Data Science and Computational Science
PRO and Related Resources
- 9:45 Darren Natale: Implementation of the PRO Sites Ontology
- 10:25 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...)
- 10:45 Break
- 11:00 Erich Baker and Elissa Chesler: GeneWeaver
- 11:30 Cindy Smith: The Alliance of Genome Resources
- 12:00 Kimberley VanAuken: Noctua
- 12:30 Lunch
PRO and Disease
Chair: Darren Natale
- 13:30 Judith Blake: Disease Ontology -- overview of available resources
- 14:00 Chris Mungall: MONARCH
- 14:30 Elissa Chesler: MGI effort to combine variant data with disease forms; Genereader resource, PRO IDs for variants
- 15:00 Break
- 15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO
- 15:45 Peter d'Eustachio : PRO and Reactome
- 16:15 Alexander Diehl: PRO, the Antibody Ontology and the Cell Ontology
- HIPC, cell populations, the Antibody Panel Ontology, Cell types vs. cell states -- when do combinations of protein markers
17:00 Debate: On the proper representation of PRO annotations
- Participants: Alan Ruttenberg, Chris Mungall, David Hill and Darren Natale. Chair: Barry Smith
- 18:00 Working dinner
Schedule: Thursday, October 12, 2017
- 8:00 Continental breakfast
GO, PRO and UniProt
Chair: Cathy Wu
- 8:45 Maria Martin (EBI): Representing UniProt
- 9:30 Chris Mungall (LBL, Berkeley): Representing GO
- 9:45 Discussion of GO, PRO and UniProt: How they will work together
- 10:30 Break
- 10:45 Julie Cowart: Writing SPARQL queries for PRO
- 11:15 Alan Ruttenberg: Enhanced SPARQL queries for PRO
- 11:45 Cecilia Arighi: The role of NLP in PRO curation
- 12:15 Lunch
13:00 Debate: How genes are referenced in OBO Foundry and in PRO: why do they differ?
- Participants; Chris Mungall, Darren Natale, Alan Ruttenberg. Chair: Barry Smith
- 14:00 Roundtable on killer apps for PRO
- 16:00 Close
Participants
*=online
- Cecilia Arighi (Delaware / PRO)*
- Erich Baker (Baylor)
- Judith Blake (JAX)
- Chuming Chen (Delaware)*
- Elissa Chesler (JAX)
- Julie Cowart (Delaware)*
- Mary Dolan (JAX)
- Peter d'Eustachio (NYU)*
- Alexander Diehl (Buffalo)
- Harold Drabkin (JAX)
- Susan Gregurick (NIH / NIGMS)*
- David Hill (JAX)
- Stanley Laulederkind (Medical College of Wisconsin)
- Peter McGarvey (Georgetown)
- Maria Martin (EBI)
- Chris Mungall (LBNL)
- Darren Natale (Georgetown)
- Li Ni (JAX)
- Karen Ross (Delaware)*
- Alan Ruttenberg (Buffalo)
- Cynthia Smith (JAX)
- Barry Smith (Buffalo)
- Kimberley VanAuken (CalTech)
- Laurens Wilming (JAX)
- Cathy Wu (Delaware / PRO)
Please contact Barry Smith for further information.
